Analysis of lipid surface area in protein-membrane systems combining voronoi tessellation and monte carlo integration methods

Takaharu Mori, Fumiko Ogushi, Yuji Sugita

    Research output: Contribution to journalArticlepeer-review

    26 Citations (Scopus)

    Abstract

    All-atom molecular dynamics (MD) simulation has become a powerful research tool to investigate structural and dynamical properties of biological membranes and membrane proteins. The lipid structures of simple membrane systems in recent MD simulations are in good agreement with those obtained by experiments. However, for protein-membrane systems, the complexity of protein-lipid interactions makes investigation of lipid structure difficult. Although the area per lipid is one of the essential structural properties in membrane systems, the area in protein-membrane systems cannot be computed easily by conventional approaches like the Voronoi tessellation method. To overcome this limitation, we propose a new method combining the two-dimensional Voronoi tessellation and Monte Carlo integration methods. This approach computes individual surface areas of lipid molecules not only in bulk lipids but also in proximity to membrane proteins. We apply the method to all-atom MD trajectories of the sarcoplasmic reticulum Ca 2+-pump and the SecY protein-conducting channel. The calculated lipid surface area is in agreement with experimental values and consistent with other structural parameters of lipid bilayers. We also observe changes in the average area per lipid induced by the conformational transition of the SecY channel. Our method is particularly useful for examining equilibration of lipids around membrane proteins and for analyzing the time course of protein-lipid interactions.

    Original languageEnglish
    Pages (from-to)286-293
    Number of pages8
    JournalJournal of Computational Chemistry
    Volume33
    Issue number3
    DOIs
    Publication statusPublished - 2012 Jan 30

    Keywords

    • Monte Carlo integration
    • Voronoi tessellation
    • area per lipid
    • lipid bilayers
    • membrane proteins
    • molecular dynamics simulations

    ASJC Scopus subject areas

    • Chemistry(all)
    • Computational Mathematics

    Fingerprint Dive into the research topics of 'Analysis of lipid surface area in protein-membrane systems combining voronoi tessellation and monte carlo integration methods'. Together they form a unique fingerprint.

    Cite this